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I don't think I can replicate this in a simple case, but I have two modules, each that operate just fine when they are the only module imported.
Builds are inside a conda environment, with visual studio 2015 64-bit as compiler. One package is this one: https://github.com/usnistgov/CEGO and the other one is an internal C++ library with a pybind11 wrapper.